Nanoscale array biomolecular bond enhancer device

ABSTRACT

The invention teaches the use of an addressable nanoscale device to create a programmable substrate useful in selectively attracting proteins, nucleating protein crystals and growing protein crystals of a size amenable to diffraction analysis. Further taught is the use of nanoscale assemblies to create charge patterns, where such charge patterns are useful in purifying, nucleating or crystallizing protein molecules. Charge extension moieties, including water, are taught. The invention provides rapid and efficient identification, purification and detection of proteins and protein-related complexes.

RELATED CASES

Not applicable.

GOVERNMENT FUNDING

Not applicable.

TECHNICAL FIELD

Biomolecular engineering, and in particular protein bonding andcrystallization

BACKGROUND

There are about 100,000 different proteins expressed in eukaryoticsystems. Protein structural models are a unique source of information:location and properties of binding sites in toxins; domain structure oflipoproteins; molecular contact and recognition. Generating correct anddetailed structural models of proteins is aided by the ability to obtainand analyze a protein in its crystal form.

Proteins are macromolecules (heteropolymers) made up from 20 differentamino acids, also referred to as residues. For proteins below about 40residues the term peptide is frequently used. A certain number ofresidues is necessary to perform a particular biochemical function, andaround 40-50 residues appears to be the lower limit for a functionaldomain size. Protein sizes range from this lower limit to severalhundred residues in multi-functional proteins.

Proteins can be several hundred residues long and fold into a3-dimensional structure. It is therefore quite understandable thatprotein molecules have irregular shapes and are not ideally suited to bestacked into a periodic lattice, i.e., a crystal. Protein crystals arethus very fragile, soft and sensitive to environmental variations.Protein crystals contain on average 50% solvent, mostly in largechannels between the stacked molecules of the crystal. The interactionsholding the molecules together are usually weak, hydrogen bonds, saltbridges, and hydrophobic interactions.

The structures of many important proteins remain a mystery simplybecause researchers are unable to obtain crystals of high enough qualityor large enough size. Generally, for useful measurements to be obtained,crystals must have dimensions of approximately 0.3 mm to 1.0 mm, and theprotein molecules must be arranged in an orderly, repeating pattern.

In order to obtain a crystal, the protein molecules must assemble into aperiodic lattice. To bring the protein molecules into close associationso that nucleation may occur, one typically starts with a solution witha high protein concentration (2-50 mg/ml) and adds reagents that reducethe solubility close to spontaneous precipitation. By slow furtherconcentration, and under conditions suitable for the formation of a fewnucleation sites, small crystals may start to grow. Often manyconditions have to be tried to succeed. This is usually done by initialscreening, followed by a systematic optimization of conditions. Crystalsshould to be sub-mm range in each direction to be useful forconventional diffraction experiments.

Other techniques for growing protein crystals, such as ‘sitting drops’,‘dialysis buttons’, and ‘gel and micro batch’ techniques are known inthe art. Devices for promoting crystallization include the hanging-drop,sitting-drop, sandwich-drop, dialysis, micro batch or microtube batchdevices (U.S. Pat. Nos. 4,886,646, 5,096,676, 5,130,105, 5,221,410 and5,400,741; Pav et al., Proteins: Structure, Function, and Genetics, 20,pp. 98-102 (1994); Chayen, Acta. Cryst., D54, pp. 8-15 (1998), Chayen,Structure, 5, pp. 1269-1274 (1997), D'Arcy et al., J. Cryst. Growth,168, pp. 175-180 (1996) and Chayen, J. Appl. Cryst., 30, pp. 198-202(1997), incorporated herein by reference). Microseeding may be used toincrease the size and quality of crystals.

In iterative drug design, crystals of a series of protein or proteincomplexes are obtained and then the three-dimensional structure of eachcrystal is solved. Such an approach provides insight into theassociation between the proteins and compounds of each complex.

Notwithstanding the variety of methods practiced, what are constantlysought are faster, less expensive methods of crystallizing biomolecules,and, in particular, proteins.

Nucleation requires higher levels of saturation than those associatedwith metastable phases amenable to crystal growth. An environment thatfavors a higher local concentration of macromolecules may lower theenergy barrier for nucleation. Compositionally modulated superlatticeshave been identified which act as potent and highly specific catalystsfor the nucleation of many different protein crystals. (See“Nanoengineered Surfaces for the Epitaxial Nucleation of ProteinCrystals”, Robert Haushalter and Ted X. Sun, Parallel SynthesisTechnologies and Alexander McPherson, Univ. of California, Irvine,CAlif.).

What is needed is a means of providing an environment that favors a highlocal concentration of the macromolecules of interest, and therebyfostering nucleation and subsequent crystallization. What is needed areways to bring protein molecules or residues in close association underconditions so as to promote the weak bonding necessary for proteincrystallization. Further, what is needed is a rapid means of calibratingconditions for a high through-put protein purification, nucleationand/or crystal growth.

What is also needed is a “bottoms up” nanoscale means to promoteprotein-protein bonding and crystal growth. What is also needed is acontrollable nanoscale environment to assemble biomolecules, includingproteins, in periodic lattice formations. What is further needed is theability to grow crystals suitable for diffraction analysis on aprogrammable nanoscale array.

What is also desired is a method for creating a surface designed forseeding organic crystals and especially protein crystals. Furtherdesired is a means to refine and purify proteins in mixtures andsolutions. What is needed are purifying devices and methods thatfacilitate protein nucleation, protein crystallization and other proteinidentification and testing steps, as well as refining or purifyingprotein-based drugs or drug-precursors.

BRIEF SUMMARY

The invention teaches the use of an addressable nanoscale array assemblyon a substrate to program a charge pattern upon a surface of thenanoscale array. The invention provides a device allowing for the chargebearing surface to be exposed to a solution containing a biomolecules ofinterest. The charge pattern upon the surface is useful in causing closeassociation of charge bearing biomolecules. Such close associationprovides, depending on a number of factors, weak bonding between themolecule of interest and the surface, as well as bonding among otherinstances of the molecule of interest, that is, inter-molecular bonding.The device may be used for purification of a molecule or protein ofinterest, or nucleation or seeding of protein crystals. The inventionprovides for protein crystal formation of a variety of sizes rangingfrom seed crystal size to protein crystals of sizes amenable todiffraction analysis in a high throughput, rapid and inexpensive manner.

The invention employs nanoscale addressable arrays (with myriad crosspoints) to create programmable charge patterns—portions of negative,positive or neutral charge. Owing to the charge attraction exerted oncharged portions of protein molecules, the nanoscale arrays chargepatterns may be configured to attract molecules with certain chargecharacteristics. Moreover, the addition of water (or other suitablehydrophobic or hydrophilic charge extension moiety or moieties)amplifies the effective range of charge and facilitates proximity andattraction of a variety of molecules of interest. The molecules ofinterest may be any biomolecules, such as a known protein beingpurified, nucleated or crystallized or an unknown protein beingcharacterized.

What is also provided is a method and device for producing andharvesting protein crystals of a variety of sizes. By producingnucleated protein crystals, such crystals can be harvested and used togrow bigger crystals. In alternative embodiments, protein crystals of asize that may be amenable to analysis for structural determination orprotein identification may also be grown.

The inventive device also provides a means to refine and purify mixturesand solutions. In one embodiment, the addressable nanoscale array deviceis positioned within a tube-like housing (or tube) or cylinder. Asolution containing molecules of interest may be flowed through thetube. The length of the cylinder may be varied, as can the diameter, andthe arrangement of the charge pattern surface on the nanoscale arrayassembly within the tube. The charge pattern on part or all of thecharge bearing surface of the nanoscale array assembly may bedynamically altered. For instance, the charge can be reversed to releasemolecules, which can then be collected by flushing through the tube andcollecting the effluent. The charge pattern can also be manipulated todirect growth of the molecule of interest.

Also provided is a multi layer nanoscale assembly array that bothprovides the topography of the surface (bottom or outermost layer) aswell as the charge pattern (upper or innermost layer).

The invention also provides addressable arrays on a suitably transparentor transmissive polymer as a substrate or array bearing material, wherethe protein associations encouraged by the surface design can beoptically or otherwise examined without transfer of the proteins thatare bound to the surface.

Other advantages, novel features, and objects of the invention willbecome apparent from the following detailed description of the inventionwhen considered in conjunction with the accompanying drawings, which areschematic and which are not intended to be drawn to scale. In thefigures, each identical or nearly identical component that isillustrated in various figures is represented by a single numeral. Forpurposes of clarity, not every component is labeled in every figure, noris every component of each embodiment of the invention shown whereillustration is not necessary to allow those of ordinary skill in theart to understand the invention.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 a depicts a water molecule and its charged regions.

FIG. 1 b alignment of water molecules in relation to charged surface.

FIG. 1 c depicts water alignment proximal to a charged surface.

FIG. 2 depicts a device according to the present invention.

FIG. 3 depicts application of a device according to the presentinvention.

FIG. 4 depicts an alternate embodiment of the invention.

FIG. 5 a and 5 b inclusive depict an alternate embodiment.

FIG. 6 a and 6 b each depict a multilayer (folded and rolled,respectively) array bearing sheet electrically connected to a logicdevice.

FIG. 7 depicts a capacitively coupled multi layer array bearing sheet.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT

INTRODUCTION. This section begins with some preliminary concepts, thenthe preferred embodiment is described, followed by a discussion of thecomponents of the preferred embodiment. Definitions are placed at theend of this section so as to facilitate the flow of the description.

PRELIMINARY CONCEPTS. Nanoscale devices can be self assembled intoperiodic lattices. Nanowires can form programmable cross bararrangements (see U.S. Pat. No. 6,586,965 to Keukes, incorporated bereference) Nanoscale arrays can form bistable switches (on/off) and canattract molecules (Leiber et al., US published application 20050117441,incorporated by reference). Many means have been described offabricating and assembling nano-arrays, including self-assembledmonolayer patterns (Leiber, US publication no. 20020117659, incorporatedby reference).

The present invention applies a novel approach to employing a nanoscaleaddressable array to produce a charge pattern to cause close associationof protein molecules. Depending on a number of factors, such closeassociation may effect a purification of a protein of interest, or mayresult in crystal nucleation or crystal seeding. Moreover, the inventionprovides a charge extension moiety, such as water, to extend the chargepattern from the surface of the nanoscale array into a predeterminedregion.

FIG. 1 a conceptually depicts the charged regions of a water molecule10: electro-positive 12 and electro-negative 14. FIGS. 1 b and 1 cconceptually depict how the electronegative and electropositive regionsof molecules such as water align in the presence of a charged surface16.

Water molecules align in the presence of a charge and assume twodistinct patterns, clathrate or layered, depending on whether moleculesare near a hydrophobic surface or near a hydrophilic surface,respectively (see Cells, Gels, and The Engines of Life by Gerald H.Pollack, Ebner & Sons, Seattle, Wash.). The pattern of water moleculesresponding to a surface charge pattern effectively extends the patterninto a three dimensional space. Thus, water is considered for thepurposes of this invention as a charge extension means. As explainedfurther below, the charge pattern extending into a fluid interior is ameans for increasing the effective attraction of protein molecules insolution and increasing the bonding of protein molecules to the surfacecharge and to other instances of the molecules from the proteincontaining solution. Referring to FIG. 1 c, one need consider the chargeattracting the water molecules to be arising from a nanoscaleaddressable array. As discussed herein, bonding to the charge bearingsurface is meant to include the surface itself as well as the extendedsurface by means of a charge extension means.

FIG. 2 shows a device 20 according to the present invention. The device20 provides a multilayer addressable array 22 on a flexible substrate sothat it may be rolled and placed within a tube-like housing 24 or fluidhandling cylinder. FIG. 3 depicts a similar device along with flow ofsolution 31. In both FIG. 2 and FIG. 3, the nanocrystallizer substrate22, 32 includes an addressable array of one (not depicted) or morelayers of nanoscale array configured with a charge pattern. The chargepattern attracts (or repels) molecules of interest from any solution(s)introduced in the tube. In this manner, the predetermined programmablecharge pattern is calculated to attract molecules from a medium exposedto the charge surface and containing molecules of interest, and to aidin the formation of a periodic lattice structure among the molecules ofinterest.

Thus the charge pattern may be considered a rationally designed surfacethat, depending on the solution or fluids introduced and the chargepattern assumed, enhances protein purification, nucleation or crystalseeding. The nanoscale programmable substrate may be a continuous sheet,may be of multiple layers, may be a series of similar patterns, or maybe a progressive pattern. In short, any variation is possible along thelength and within the interior of the container of the nanosubstrates.Moreover, the nanosubstrates may be statically charged or subject todynamic charging in the course of exposure to the molecule of interest.

Consistent with the device discussed hereinabove, the invention providesa method of using a nanoscale assembly to promote bonding amongmolecules of interest, said method comprising the steps of programming acharge pattern on a surface of said nanoscale assembly, said chargepattern enabled by means of one or more addressable nanoscale arrays inthe nanoscale assembly; and by means of a fluid medium containing atleast one variety of a molecule of interest, exposing the molecule ofinterest to charge pattern on said nanoscale array, so as to foster bondformations between molecules of interest. In addition, the method mayinclude adding a charge extension moiety (e.g., water) and may involveanalyzing the collected molecule in situ (still attached to a substrate)or reversing or neutralizing and washing the protein aggregate, whetheror not in crystal form, into an effluent for analysis, identificationand/or characterization.

The invention reduces the need for engineering attachment points intothe large protein molecules; it has the advantages of low cost and highefficacy in purification, crystallization and other identification ormodification steps within a single device

Referring to FIG. 4, an alternate embodiment (denominated a “chip” 40for ease of reference) is one or more addressable array devices within apredetermined array reservoir 44 in a plate 41 containing fluidreservoirs 42 and solution of interest reservoir 43. As depicted in FIG.4, the reservoirs 42, 43 have a flow channel at least with the arrayreservoir 44, which in turn has an aperture for outflow 46. The sequenceof flow from reservoirs 42, 43 to and through the array reservoir 44varies according to the protocol. By controlled introduction into thearray reservoir 44, the conditions for growth and any subsequentprocessing (e.g., wash, rinse, etc.) can be carefully manipulated.

An alternate embodiment as depicted in FIGS. 5 a and 5 b is a multilayer array that provides the topography of the surface (bottom oroutermost layer) as well as the charge pattern (upper or innermostlayer). Taken together, FIGS. 5 a and 5 b depict an alternate embodiment50 wherein at least two layers of addressable arrays form both the arraysurface shape and the charge pattern. A first substrate 51 bears a firstnanoscale addressable array layer 52 which in turn bears anelectro-restrictive polymer layer 53, a conductive contact layer 54, asecond substrate 55 and a second addressable array layer 56.

FIG. 5 b depicts the embodiment as in FIG. 5 a wherein charge patternsare imposed on the first and second addressable array layers 52, 56 aremodified so as to be a charge patterned first addressable array layer520 and a charge patterned second addressable array layer 560. In thepresence of a charged patterned first addressable array layer 520, theelectrorestrictive polymer layer changes shape by contracting. Such acontraction pattern creates relatively lower and higher points whichtranslate into wells and plateaus in the regions of the secondaddressable array layer 56, 560. Thus, proteins attracted to the chargepatterned second array layer 560 can be oriented in wells created by thecharge patterned first array layer 520

In cases where some or all of the substrates bearing addressable arraysare transparent polymer, the protein associations encouraged by thesurface design can be optically examined without transfer of theproteins. The simplicity and economy of this one device to both captureand examine proteins and protein crystals permits heretofore unexpectedspeed in high throughput applications.

To obtain seed crystals suitable for X-ray diffraction, iterations onnanoscale seeding in a progressively larger growth area may beperformed. According to the invention, any addressable array on asubstrate could initially define a region suitable for, say, severaldozen molecules as may characterize nucleation. By rearranging thecharge pattern, the region could expand to include progressively largerareas, and additional deposition of protein solution may be indicated tofeed crystal growth. Moreover, it may be useful to exploit a flexiblearray surface to gradually increase or decrease the curvature of thearray substrate, or otherwise manipulate the shape to further enhancedesired crystal proportions. In this manner, it may be possible toobtain the large single crystal useful in classic diffraction analysis.

Collection and Seeding. The protein of interest may be released from theaddressable array surface simply by a neutralization of the attractantcharge. Alternatively, an appropriate fluid wash may gently slough theprotein molecules off the array. In an alternate embodiment, the proteinmay be processed without detaching it from the array surface. In caseswhere the protein structure will be used to further seed largercrystals, the array surface or a small portion of a large array surfacemay be cut and inserted into, for example, a hanging drop or othercrystallization technique.

The invention is contemplated to include both reusable nanoscale arrays(where after harvesting of the seed crystals or protein, the array maybe rinsed and re-used) and disposable array devices (where perhapsbiohazard dictates single use). Pre-calibrated diagnostic chips or otherpre-packaged arrays may also be usefully constructed using the inventivedevice. So too the transparent crystallizer which may become thesubstrate of an optical characterization process (a combinedcrystallization—analysis chamber) is apparent to one of skill in therelevant art. Whether for classic diffraction or for yet to bepopularized nano diffraction analysis, the nanoscale array crystallizercomposed of transparent elements may be remarkably efficient andeconomical.

Supplemental Description. At this point we provide additional backgrounduseful to practicing the invention taught herein.

Assembling the Array. The invention teaches an addressable nanoscalearray operable to adopt a predetermined charge pattern, thereby creatinga surface designed to enhance protein nucleation and protein crystalformation. Any of the methods discussed herein above, or otherwiseknown, for creating addressable nanoscale arrays are suitable. One arrayassembly method is set forth below.

Nanoscale devices. In one embodiment, silicon nanowires are used as thenanoscale devices. Various methods of nanowire production exist, andthis invention is not limited as to the manner in which nanowires areproduced. Typically the nanowire diameters are of about 3 to 50nanometers; wire length about 10 to 100 microns. An array consists ofabout 1,000×1,000 nanowires, or a plurality of electrically connectednanoscale devices providing the functional equivalent of 1,000×1000nanowires.

In one embodiment, the nanowire for the invention is a core-shell (Siinner, Ge outer) and the array would include a first layer of conductivewires, and a second layer of the Si-Ge core shell wires. Other compoundsemiconductor materials including Gallium Arsenide, GaAs, and IndiumPhosphide, InP, can also be used. CdS nanowires, Cu₂S/CdS core-shellstructures, Cu₂S with Au nanoparticles and other combinations can alsobe used.

Transmissive and transparent material. Any material transmissive of aradiant energy may be selected. In one embodiment, the transparentmaterial is a bi-axial oriented polyethylene terephthalate (BOPET)polyester film. The transparent medium is provided in sheets, and thesheet thickness can vary. Individual sheets may be thin (about 100nanometers) or of a thickness three or more time greater: approximately300 or more nanometers. In one embodiment, the inter-sheet and theinter-wire distance ideally are close to being equal.

Array assembly method. A general approach for depositing addressablearrays on a sheet is described as follows. First, a sheet is selected.The preferred method of getting the nanoscale devices parallel to afirst surface of a given polymer sheet is that used to create aLangmuir-Blodgett (LB) film. An LB film is a monolayer, a set ofmonolayers, or a multilayer deposited from liquid onto a solid substratewherein the resulting film properties are controllable. As applied tothis invention, the next two steps are: a first swipe of a sheet througha suspension of nanowires or nanoscale devices whereby a first layer ofnanoscale devices are deposited on the mylar surface in a parallelalignment; and a second swipe through such a suspension, orienting thesheet at a rotation from the first swipe, resulting in a second layer incrossbar formation with respect to the first layer. The variations tothis general method of nanodevice deposition and crossbar formation willbe apparent to those of skill in the relevant art, and are included inthe invention as taught herein.

The two nanodevice layers in cross bar formation comprise an addressablearray. Once the array is formed, if only a single sheet is to be used,then the next step is connection to a logic device. Such connection maybe accomplished with known lithographic techniques, and small-scale wireleads from the array to a logic device which, in turn, preferablyconnects to a recording media such as flash memory or hard disk.

In the multilayer embodiments, the step of stacking sheets or folding asheet or sheets to produce any number of layers may be performed beforeconnectivity to a logic device.

Folding and Rolling. It is apparent that a sheet of 100 nanometersthickness and a square meter in size, folded ten times results in a cube1 mm thick with 1,000 layers of array-bearing sheets. Alternatively, asheet can be rolled or folded in one direction and sliced at 1 mmintervals, yielding 1 mm×1 mm×1 mm shapes. Cube, ellipse or cylinder: noshape requirement need be imposed. A sphere or any other shape may beused; at present a cube is preferred. In an alternate embodiment, layersare stacked in a skewed fashion, that is to say, aligned at an offset orotherwise adjusted in orientation so as to reduce shadow effects. Otherways of stacking and assembling array-bearing-sheets so as to minimizeshadow and alternate sheet stacking configurations will be apparent tothose of skill in the relevant art.

One can appreciate that a “roll” assembly method is fairly similar to a“fold” when considering on the order of one thousand layers. In a largescale operation the step of cutting after rolling or folding isincluded. Of course, one could just make one thousand or so separatelayers and simply stack them up (without any explicit folding orrolling). Any and all such assembly techniques are intended to beincluded herein.

Connectivity. The currently preferred lithographic approach toelectrically coupling the addressable array is described in U.S. Pat.No. 6,963,077, issued to inventors De Hon, et al., entitled“Sublithographic Nanoscale Memory Architecture” (incorporated herein byreference). Microscale devices, typically wires, are in connectiveassociation with the addressable array.

FIG. 6 a and 6 b inclusive illustrates a multilayer embodiment of theimaging device and connectivity to a logic device. In FIG. 6 a thearray-bearing sheet 60 was folded, in 6 b the array-bearing sheet 60 wasrolled in one direction and leaving a slight tongue 61 or tag protrudingfrom the roll in each case. A first set of microscale devices (notdepicted) on the tongue 61 connects the addressable array by means of asecond set of microscale devices 65 connecting the array to the logicdevice 66.

FIG. 7 depicts one connectivity embodiment of an array-bearing sheet ina layered formation via capacitive conductance. A first set ofmicroscale devices 75 run down a face of the cube-formed multilayerarray bearing sheet 70. The connectivity to the logic device 76 is bymeans of capacitive conductance. Capacitive conductance connectivityobviates the need for a second set of microscale devices and avoids theexposure to heat suffered during most conventional lithographicprocedures. Standard CMOS chip pads (not depicted) are used andno-direct coupling to the array bearing substrate is needed.

Configuring the Array. One alternative method of configuring the arrayis to set a charge pattern at a distance consistent with one or moreprotein structure habits. In the case where some structure informationexists, the distances between repeating charge elements may becalculated to correspond to surface hydrophobic or hydrophilic regions.In protocols where an unknown is being attracted, then a gradient may beused and, by iterative steps, an optimized pattern derived.

Solution Preparation. Those of skill in the relevant art are familiarwith methods of preparing dilutions conducive to protein purification orcrystal formation.

Solution Deposition. Where the embodiment is other than a “flow through”device, one alternative method of depositing the solution (fluid medium)is immersion of the array in a solution of interest, perhaps in amicro-titer plate or similar tray-like device. In the alternateembodiment depicted in FIGS. 5 a and 5 b, inclusive, the upper chargebearing surface may be a nano-topography including nano-wells and spacein between the nano-wells. One solution dispensing option ismicrofluidic depositions in the nano-wells by means that are currentlyused in applications such as ink jet. The fluid medium may contain notonly the molecule of interest, but may also contain seed crystals, orperiodic lattices of the molecule of interest.

Current fluid techniques applied in inkjet approaches can be engaged inapplication of droplets on a nano scale array. Both the direction andamount of liquid can be controlled in each droplet by print heads suchas those made by Dimatix. Using such a multiple drop approach, a rangeof dilutions can be automatically and repeatable deposited for largescale throughput of a protein of interest or a sample for identificationor characterization.

The invention is intended to be inclusive of techniques known in the artconcerning crystal growth conditions. It would be readily apparent toone of skill in the art to vary the crystallization conditions disclosedabove to identify other crystallization conditions that would produceseed crystals. Such variations include, but are not limited to,adjusting pH, protein concentration and/or crystallization temperature,changing the identity or concentration of salt and/or precipitant used,using a different method for crystallization, or introducing additivessuch as detergents (e.g., TWEEN 20 (monolaurate), LDOA, Brji 30 (4lauryl ether)), sugars (e.g., glucose, maltose), organic compounds(e.g., dioxane, dimethylformamide), lanthanide ions, or poly-ioniccompounds that aid in crystallizations. High throughput crystallizationassays may also be used to assist in finding or optimizing thecrystallization condition.

Definitions: A selection of key terms as they are to be understoodherein, including the specification, drawings and claims, are definedbelow for reader convenience. A definition in the singular includes theplural.

Addressable array: a nanoscale cross bar array as defined by Leiber etal. US publication number 20050117441 (incorporated herein byreference), which is addressable. The addressable array may be composedof nanoscale devices, such as, for example nanowires or any nanowirelike devices capable of creating a charge pattern, as well as a meansfor connecting the nanoscale devices to microscale input/output. Someapproaches for such nano-microlithography are taught in U.S. Pat. No.6,963,077 (incorporated herein by reference) and are compatible with thedevice taught herein. Herein, “array” means “addressable array” unlessexplicitly stated otherwise.

Array-bearing sheet: any suitable material of a predetermined thicknessbearing at least one addressable array, wherein said array includes somenanowire-like or other nanoscale devices capable of creating a chargepattern.

Capacitive coupling: a means for electrically connecting devices; see,e.g., “Manufacturability of Capacitively Coupled Multichip Modules”,Thomas F. Knight, Ph.D. and David B. Salzman, Ph.D. 1994 IEEE pp.605-608 (incorporated herein by reference).

Langmuir-Blodgett: a process or set of processes amenable for a widevariety of applications and particularly adaptable for depositingnanoscale devices in a crossbar array on selected sheet material.

Logic device: any device capable of operatively interacting with theaddressable array and performing all or some of the functions ofamplifying, storing, processing, and transmitting the output from theaddressable array. Includes, but is not limited to, CMOS family ofintegrated circuits.

Microscale fabrication devices: microscale wires or the equivalent inconductive association with at least one addressable array.

Nano: “nano”, alone or in combination with “scale” (i.e. nanoscale) orany other term, is meant to include elements of widths or diameters ofless than 1.mu.m

Nanowire: structures as described by Leiber USPTO publication number20050117441 (incorporated herein by reference). A “wire” refers to anymaterial or combination of materials having a conductivity of anysemiconductor or any metal including, but not limited to nanorods,nanowires, organic and inorganic conductive and semiconducting polymers.Moreover, as used herein, “nanowire” also means any nanowire or nanowirelike element, and includes but is not limited to semiconductor nanowire,nanowire core-shell structure, nanowire heterojunction, or junctionbetween nanowire and other material, including metal or polymer.Semiconductors used include the standard list (Si, GaAs, etc.) as wellas any compositions from which an addressable array may be formed. Onealternative embodiment uses core-shell nanowires.

Nanoscale device: any device of nano dimensions capable of homogenouslyor heterogeneously participating in an addressable array. As usedherein, participation is understood to mean directly or indirectlycontributing to a charge pattern. A nanoscale device may be composed, inwhole or in part, of nanowires.

Stack (stacking): two or more array-bearing sheets closely associated insuch a manner so that conditions enabling a volumetric hologram exist;process of bringing about such an association of array-bearing sheets.

Transparent medium: any transparent material suitable for sheetformation and capable of bearing an addressable array, the preferredtransparent material is a biaxially-oriented polyethylene terephthalate(BOPET) polyester film.

The present invention is not limited to given embodiments or examples.Rather, the invention is intended to include all that is described anddepicted, or set forth in the attached set of claims, along with theequivalents thereto, that define possible further embodiments for aperson skilled in the art.

1. A method of using a nanoscale device to promote bonding amongmolecules of interest, said method comprising the steps of: a)programming a charge pattern on a surface of said nanoscale device, saidcharge pattern enabled by means of one or more addressable nanoscalearrays in the nanoscale assembly; and b) exposing, by means of a fluidmedium where said medium contains at least one variety of a molecule ofinterest, said variety of molecule of interest to charge pattern on saidnanoscale array, so as to promote bond formations between molecules ofinterest.
 2. A method as in claim 1 further including the intermediatestep of introducing a charge extension moiety to the charged surface ofthe nanoscale array, so that said charge extension moiety extends thecharge pattern a further distance from the surface of the nanoscaleassembly.
 3. A method as in claim 2 in which the charge extension moietyis water.
 4. A method as in claim 1 wherein the step of exposing saidvariety of molecule of interest includes the sub step of deposition ofsaid fluid medium containing molecule in predetermined concentrationscontrollably upon the nanoscale assembly surface.
 5. A method as inclaim 4 wherein said concentrations may be a range of dilutions of themolecule of interest.
 6. A method as in claim 1 further including thestep of harvesting said variety of molecule of interest wherein the stepof harvesting includes altering the charge pattern on at least a portionof the addressable nanoscale array.
 7. A method as in claim 1 whereinthe fluid medium is controllable with respect to a plurality ofconditions, including any or all of: pH, temperature, concentration,salt, additives.
 8. A method as in claim 7 wherein the conditionspromote biomolecules in organized structures of dimensions ofapproximately 0.3 mm to 1.0 mm in each direction.
 9. A device forpromoting the bonding of biomolecules comprising: an addressablenanoscale array wherein a charge pattern is impossible on a firstsurface; means for dispensing a fluid containing a molecule of intereston the first surface of the addressable nanoscale array such thatbonding between instances of the molecule of interest is fostered,thereby promoting bonding of said molecules.
 10. A device as in claim 9wherein said bonding promotes arrangement of the molecule of interestamenable to crystal growth of the molecule of interest.
 11. A device asin claim 10 further comprising a surface charge pattern extension meansto selectably extend a surface charge pattern.
 12. A device as in claim11 where the surface charge pattern effects positioning of proteinmolecules.
 13. A device as in claim 12 where the resultant positionedprotein molecules are suitable for analysis.
 14. A device as in claim 12wherein the surface charge pattern is dynamically addressable.
 15. Adevice as in claim 9 wherein the fluid containing the molecule ofinterest comprises said molecule of interest arranged in a periodiclattice structure.
 16. A device for improved purification ofbiomolecules, said device comprising: a nanoscale substrate programmablewith charge patterns for selective molecule attraction; a means ofexposing biomolecules, where said biomolecules are in a form amenable toa directable flow, to the nanoscale substrate in a manner such that thebiomolecules may be collected, thereby improving purification of saidbiomolecules.
 17. A device as in claim 16 wherein the device includes atube-like housing into which the nanoscale substrate is positioned suchthat the biomolecules flow within the tube and wherein the chargepattern extends to the center of the tube.
 18. A device as in claim 17wherein the length of the tube-like housing facilitates differentialprogramming of the charge pattern on said nanoscale substrate atpredetermined sections of the tube.
 19. A device as in claim 16 whereinthe preselected material is transmissive.
 20. A device as in claim 19wherein the preselected material is optically transmissive.
 21. A deviceas in claim 16 wherein the preselected support material comprises a chipupon which are a plurality of reservoirs, at least one nanoscale arraycontaining reservoir, at least one fluid containing reservoir, and atleast one biomolecule containing reservoir, wherein each biomoleculecontaining reservoir and each fluid containing reservoir is connected toat least one nanoscale containing reservoir through a channel, wheresaid exposure of biomolecule to the nanoscale array is enabled by theconnection between said biomolecules containing reservoir and saidnanoscale array containing reservoir.